How to solve the performance/memory issues related with having entities that depend on other entities in DDD?

Since you mention DDD: if there are two repositories it indicates that there are two Aggregate Roots . The whole point of the Aggregate Root concept is that each root is responsible for its entire object graph .

There is no standard way. This is domain driven design, so it depends on the domain, if you ask me. Maybe you could add some more domain to your design.

You only have two concepts: a Project and a File. But you say you don't want to load the file (assuming that File will always load the content of the file).

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